sbatch_mriqc.sh

#!/bin/bash

# Add your SLURM options here

#SBATCH --cpus-per-task=8 # Number of cores to use
#SBATCH --mem=16gb # Memory limit
#SBATCH --time=02:00:00 # Time limit hh:mm:ss
#SBATCH -e error_%A_%a.log # Standard error
#SBATCH -o output_%A_%a.log # Standard output
#SBATCH --job-name=mriqc # Descriptive job name
#SBATCH --partition=serial # Use a serial partition 24 cores/7days


##### load required modules

module load singularity

# Add commands needed to run mriqc

singularity run --cleanenv \
--bind /scratch/psyc5171/exercises/mbdata/bids:/data \
--bind /scratch/amw17004/hw3/out:/out \
/scratch/psyc5171/containers/mriqc_latest.sif \
/data /out participant